From 46c0cc357737ca7033eac7f5d6ca6b03a395ec1c Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Mon, 2 Jan 2017 21:40:01 -0500
Subject: [PATCH 1/2] move tmpdir_for_func to utils module

---
 test/conftest.py |  7 +------
 test/utils.py    | 13 ++++++++++++-
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/test/conftest.py b/test/conftest.py
index 8bca5f3..c4c2a48 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -6,17 +6,12 @@
 from snakemake.shell import shell
 from snakemake.utils import makedirs
 from lcdblib.snakemake import aligners
-from utils import run, dpath, symlink_in_tempdir
+from utils import run, dpath, symlink_in_tempdir, tmpdir_for_func
 
 # test data url
 URL = 'https://github.com/lcdb/lcdb-test-data/blob/master/data/{}?raw=true'
 
 
-def tmpdir_for_func(factory):
-    caller = inspect.stack()[1][3]
-    return str(factory.mktemp(caller))
-
-
 def _download_file(fn, d):
     """
     Intended to be called from a pytest.fixture function below.
diff --git a/test/utils.py b/test/utils.py
index 5934e08..251bd7e 100644
--- a/test/utils.py
+++ b/test/utils.py
@@ -11,15 +11,26 @@
 import urllib
 import shutil
 import shlex
+import inspect
 
 import pytest
 from snakemake import snakemake
 from snakemake.shell import shell
 
-
 SCRIPTPATH = shutil.which('snakemake')
 
 
+
+def tmpdir_for_func(factory):
+    """
+    Returns a tempdir named after the calling function.
+
+    `factory` is a pytest.tmpdir_factory instance.
+    """
+    caller = inspect.stack()[1][3]
+    return str(factory.mktemp(caller))
+
+
 def dpath(path):
     "path relative to this file"
     return os.path.realpath(os.path.join(os.path.dirname(__file__), path))

From 79fcc43cd72c9e78d216876d54e11cee91ee8eb8 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Mon, 2 Jan 2017 21:46:05 -0500
Subject: [PATCH 2/2] add test_toy.py

---
 test/test_toy.py | 100 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 test/test_toy.py

diff --git a/test/test_toy.py b/test/test_toy.py
new file mode 100644
index 0000000..a8e63a1
--- /dev/null
+++ b/test/test_toy.py
@@ -0,0 +1,100 @@
+import os
+from textwrap import dedent
+import pytest
+import utils
+
+# Each module has a config dict
+config = dict()
+
+
+def generic_fixture(key, mapping, factory):
+    """
+    Tries to handle as much of the magic as possible.
+
+    Parameters
+    ----------
+    key : str
+        Key into the module-level config dict
+
+    mapping : dict
+        Maps paths from fixtures to input files expected by the snakefile
+
+    tmpdir : str
+        Path to temporary dir, usually created by utils.tmpdir_for_func
+
+    Returns
+    -------
+    After a successful Snakemake run, returns the dictionary of the config's
+    `output` key but with paths fixed to be relative to tmpdir. This returned
+    dict is ready to be used as a fixture by test functions.
+    """
+    conf = config[key]
+    tmpdir = utils.tmpdir_for_func(factory)
+    input_data_func = utils.symlink_in_tempdir(mapping)
+    utils.run(utils.dpath(conf['wrapper']), conf['snakefile'], None, input_data_func, tmpdir)
+    output = conf['output'].copy()
+    for k, v in output.items():
+        output[k] = os.path.join(tmpdir, v)
+    return output
+
+
+# In order for the doc generation to find this config info without re-running
+# all tests, it needs to be in the module-level dict. It similarly can't be
+# added during the fixture function's runtime.
+#
+# However, the mapping and tmpdir must be provided by the function, so the
+# config and the function are tightly coupled.
+#
+# So we add the item to the dictionary here, right above the function that will
+# be using it to keep them tightly coupled in the file.
+config['hisat2_index'] = dict(
+    description="Basic example of generating a hisat2 index",
+    wrapper="../wrappers/hisat2/build",
+    snakefile="""
+      rule hisat2_build:
+          input:
+              fasta="2L.fa"
+          output:
+              index=expand("hisat2_index/assembly.{n}.ht2", n=range(1,9))
+          log: "hisat.log"
+          wrapper: "file://wrapper"
+    """,
+    output={'prefix': 'hisat2_index/assembly'}
+)
+
+
+# All the hard work is done in the config and in generic_fixture(). Now we just
+# need to set up the correct mapping of fixtures to input files.
+@pytest.fixture(scope='module')
+def hisat2_index(tmpdir_factory, dm6_fa):
+    mapping = {dm6_fa: '2L.fa'}
+    return generic_fixture('hisat2_index', mapping, tmpdir_factory)
+
+# The actual test.
+def test_index(hisat2_index):
+    assert os.path.exists(hisat2_index['prefix'] + '.1.ht2')
+
+
+def extract_examples_for_wrapper(wrapper):
+    """
+    Returns the examples for the wrapper in markdown format.
+
+    Parameters
+    ----------
+    wrapper : str
+        Expected to be the value of one of the config dict's `wrapper` keys.
+    """
+    markdown = []
+    for k, v in config.items():
+        if v['wrapper'] != wrapper:
+            continue
+        snakefile = dedent(v['snakefile'])
+        markdown.append(
+            dedent(
+                """
+                {}
+
+                ```python""".format(v['description'])))
+        markdown.append(snakefile)
+        markdown.append("```")
+    return "\n".join(markdown)